Discussion of everything related to the Theory of Evolution.
From Fitness to Optimality:
The Back Swing of Darwinism's Clock
From: DSS EXPRESS http://www.brainecology.net/ktjh/show.asp?bh=36
This year is the 200th anniversary of Darwin's birth and the 150th anniversary of the publication of The Origin of Species.
Looking back at the developmental history of biological thinking over the 150 years since the publication of The Origin of Species, we noticed that the pendulum of Darwinian clock has meaningfully swung back. In a recent published preliminary report The Development of the Neo-adaptationist Biology, written by Brain & Ecology Comparative Group (BECG), this phenomenon and its significance were analyzed on the background of biological history.
The report mentioned that Darwin in his book did not define and use the concept "adaptation". But in the discourse he repeatedly used a comparative term, the "fittest". This shows that, in Darwin's thinking, adaptation is more appropriate as a relative or referenced standard. This is the original point of the "Darwinian clock". Half a century later, based on Darwinian "fittest" idea, the Modern Synthesis proposed that using "reproduction" to measure different organisms' adaptation levels, in order to solve the issues in quantitative analysis of adaptation. Thus they created the measurable concept "fitness". This change marked the focus of evolutionary biology was shifted from phenotypic comparison of Darwin's times into genotype's comparison of the modern era, marking the "Darwinian clock" pendulum has swung away from the original point.
This in essence turns from the phenotype determinism to the gene determinism. It has a historical background that due to there is a substantially fuzziness in evolutionism on the micro-process of organisms' variation, the Modern Synthesis on the basis of genetics introduced the genetic variation theory to give a micro-empirical support for the natural selection model in explaining the causes of adaptation, and this revived the once depressed evolutionism to become a basic tool of biology with extensive explanation power. Therefore, as a theoretical result of the micro-biology times, the Modern Synthesis naturally replaced the original position of the traditional evolutionism. Moreover by abandoning phenotype, the "fitness" concept showed the self-confidence of the "genetic determinism" theory.
Particularly, the report explained why the prosperity of the Modern Synthesis had remained for 80 years. The cause is that the genetic determinism implies a tacit principle: as long as the mutation of gene was able to be passed to future generations, the predevelopmental primordial germ cells of the offspring may be automatically led by its own developmental mechanics and phenotypically express the mutated gene. However, the disproportionate suppression of population dispersal by natural selection does not directly target at gene, but targets at gene's carrier (phenotype). And it is not a selection aiming at one trait of the phenotype, but a holistic selection aiming at the phenotype carrier.
This latent principle is the most fatal flaw of the Modern Synthesis. Therefore, the in-depth problem emerges. Why is this phenotype being selected rather than that one? How is the physio-ecological process proceeding when a phenotype is selected in a concrete environment? Thus, the issue of adaptation comes back from gene to phenotype again, and returns to the traditional question: how each phenotype was selected in its life-history under different natural conditions? The Modern Synthesis encounters an insurmountable barrier in theoretical explanation.
In the report, BECG focused on the development of intraspecific comparative biology, put forward the neo-adaptationist analysis of phenotypic "optimality", and created a new comparative idea: adaptation is phenotype-centered, and it refers to organism's morphological structures and physiological functions etc. presenting optimality in using environmental resources and resisting environmental stress under specific ecological niche. This analysis can be use to measure organisms' adaptation level. Comparing with Modern Synthesis's "fitness", "optimality" concept inherits the Darwin's original idea "fittest", how degagely the pendulum of "Darwinian clock" swings back to the original position 150 years later.
The report suggest that the biotic adaptation ology is only a half-done and rough theoretical framework, and the evolutionism has just succeeded in creating an adaptation theory at the ecology level, but the physiology-leveled ology remains to be formed. Therefore the intraspecific adaptation biology shows its historical significance, it has a distinct emphasis on the physiology-leveled adaptation. On the one hand, it inherits the historical tradition of adaptation comparative study. The other hand, it entirely enters into micro-physiological process. Thereby neo-adaptationism is the another new synthesis following the evolutionism and the Modern Synthesis.
It's Friday. I've read the above three times and it is an excellent example of obfuscation.
I think what it says is that the Modern Synthesis is wrong because Darwin, writing decades before the development of the Modern Synthesis, didn't know about Mendelian Genetics and therefore our understanding of the way in which natural selection works is wrong. Perhaps I've miss-interpreted this though. I feel a metaphor coming on, would this be like saying modern man's understanding of the laws of motion are wrong because pre-historic humans didn't understand how to build a clock?
Wellalt - could you explain it more clearly please?
Good questions, Dougal. Here is another one about that. Maybe better for your understanding.
Intraspecific Adaptation Biology: A New Separated Direction
Aestivation is an important period included within the life cycle of tropical earthworms. Almost all earthworm species display this mechanism as a response to seasonal changes in soil moisture and temperature. During this phase of inactivity individuals remain at deeper soil layers, fasting and immobile. A Comparative study on the earthworms’ life cycle physiology in relation to the environmental changes, researcher can find that aestivation is a case of intraspecific adaptive strategy. The benefit is that aestivation enables individuals to reduce their demands on nutrition and energy, so that the earthworms can escape from unsuitable seasonal conditions.
Since the second half of the 20th century, in the borderland of Ecology, a large number of intraspecific adaptive strategies have respectively been found. For example, environmental changes may lead to adjusted seed size, varied number of offspring, advanced or delayed reproductive timing, diversified sizes of individuals, altered shape and behavior etc. The common nature of them is intraspecific traits and functions variation under the impact of environmental factors.
In the preliminary report The Development of the Neo-adaptationist Biology, which was recently published by BECG, the studies of intraspecific adaptive strategies have been summarized. They are from five fields, life history evolutionary ecology, behavioral ecology, adversity and stress biology, phenotypic plasticity study, evolution and pathophysiology.
The report considered that the traditional evolutionary biology research, for a long time, is based on the comparison between one species and another species; but the study of intraspecific adaptive strategy leads the variation and adaptation research into inner species. This trend has already been widespread, but hasn’t got the deserved theoretical summary and denomination.
In the preliminary report, BECG has made a comparison about the characteristics between this new research direction and the Modern Synthesis. They proposed that this new direction was gradually independent and separated from the Modern Synthesis during its germination and formation, and it has three characteristics:
(1) Its independence is firstly presented in that it discards the gene-centered view of Modern Synthesis and turns to emphasize phenotype.
(2) It introduces the strategy idea into the intraspecific phenotypic comparative study, and then moves to the microbiological level, introducing the strategy idea into the research of micro physio-ecological adaptation.
(3) It abandons the fitness analytic framework of the Modern Synthesis, adopting a new analytic framework of optimality.
BECG believed that with the three characteristics, the intraspecific adaptive biology has formed its own basic methods and patterns, and this marks its independence from the Modern Synthesis. It can be defined as: intraspecific phenotypic optimality study based on comparative physio-ecological strategy and microphysiology. BECG suggested naming it as “neo-adaptationism”, to distinguish it with the Modern Synthesis Darwinism.
The report enthusiastically appraised the neo-adaptationism, believing that the most significant is that it introduces the Darwinian paradigm into the intraspecific or inner-life-historical short-term phenotypic and microphysiological adaptations studies. The effective response mechanism, which is built up within organisms and targets at environmental changes and pressures during life history, is essentially the internal adaptive modulation mechanism at physiological level, a complex issue ignored or avoided for a long time by the previous evolutionary biologists. Thus, the emergence and the further development of intraspecific adaptive biology will provide new perspectives theoretically and experimentally to research fields such as molecular biology, physiology, neuroscience, developmental biology, evolutionary biology etc. By the historical experience of previous science, the formation of a new cognition pattern with profound empirical evidences may often give important influence and impetus on the relevant disciplines.
In general I'm still struggling to understand what you are trying to say, rather than quoting these difficult to follow texts, could you paraphrase for me?
Specifically I don't see how this example of the earthworm can't be easily explained by mainstream ideas about NS and adaptation....
Well,I’am not the member of BECG , but I’am a assentient of PD. Let me trying to make it clear.
Genetics is only successful to explain the development and reproduction of organisms, as well as the intraspecific diversity. However, it does not successfully make out the
biological variability between species, physiological adaptation, and evolution. The former is proved and the fact , and the latter hypothesis and conjecture.
MD trying to use genetics to explain the biological evolution, but has not obtain the
experimental evidence of interspecific variation and evolution. Therefore, it is a guess.
The intraspecific comparative biology , However,is creating a new analysis system, it mainly relies on the measurement and comparison to the differences of physiological phenotype. And its model directly inherite Darwin’s, but its knowledge belong to modern biology, especially micro-physiology. This research direction is successfully in the interpretation of intraspecies diversity of physiological adaptation, and it shows another new route for the Darwinian development.
Dougal,Would you please gave your explaination of the earthworm example by the mainstream ideas about NS and adaptation easily ?
I'm not sure I see the "problem" with the Modern Synthesis that is being addressed by this new analysis system:
1. The phenotype is dependent on the genotype. Evolution does not occur if selected traits are not inheritable. Phenotypes are not inherited, genotypes are.
2. The earthworm example is explainable by modern evolution theory. If the worm is able to survive a poor environment and wait until conditions are more optimal to reproduce, its fitness (as measured by reproductive success) will be greater.
3. How does one compare the "adaptive" level of two different indivduals or species without using reproductive success as the measurement?
In fact, robsabba, I could also use your same words to analyze adaptability before several months.
After I have read BECG books, I have begun to rethink the MD or MS’ analysis methods.
1．The extension of phenotype is larger than genotype. Because only parts of the phenotype can be decided by genotype , the others by “neuronal type or hormonal type”. Therefore, the view “phenotype is dependent on genotype”has become obsolete. The new biology experiments and field observations have found much phenomena, such as phenotypic plasticity, neural plasticity etc., which can not be explained by the traditional genotype theory. These phenomena in fact "be selected and be not inherited."
2． The earthworm aestivation, obviously is a physiological regulation in the body, the force of hormones is greater than genes. We can still measure their adaptation level without using reproductive success,for example, measuring the the duration of estivation ,or frequency of repeat aestivation, or survival rate after aestivation.
3．The research of modern ecology and physiological ecology, for example,ecological
strategies, stress and resistance, phenotypic plasticity, have found a lot of measure to
compare adaptation level effectively without using reproductive success.
Now I'm re-reading the third volume of the BECG works, which has put forward a new theory on the relationship between genotype and phenotype. let me make some preparations to translate it from Chineses to English, and then introduced it to everybody.
The concept of genotype determining phenotype is hardly obsolete. It has been modified with the understanding that some alterations in DNA, such as methylation, can be inherited. However, these modifications are not permanent. Phenotypic plasticity is nothing new, but this response to the environment is itself determined by the genome. The fact remains that changes that are not inherited do not constitute evolution.
All well and good, but how are such comparisons better indicators of adaption than reproductive success? It is only really of benfit if it increases reproductive success.
But how do you do this, practically speaking? How do you come up with a non-arbitrary way of making such comparisions? What is the standard for a "better adaption" if not reproductive success?
1.Since you agree with that the concept of genes determine phenotype has been modified, it shows that you have already begun to accept that the strong orthodox theory is flawed. At least it needs to complement something. The studies of alterations in DNA are only one direction of these complement. BECG’s research is another one. They are all in front,and have their own different evidence and advantage.
2.About “Phenotypic plasticity is nothing new,”
---On the contrary, there are much new things need to discover and explain in the field of phenotypic plasticity, that is the area in the ascendant. In particular, this research has been completely broken the concept that gene is the blueprint for development. (attached another DSS EXPRESS news )
3.About reproductive success, it is flawed. Animal reproductive plasticity have found that, in difficult circumstances, animals may temporarily abandon their procreation, or to reduce
the amount of their offspring , or to make their offspring smaller in body. This regulation is the best adaptation in this environment. I don’t think this regulation is not optimal because of their reduceing the reproductive success rate.
From Phenotypic Plasticity to Deep Structure
——New Approach of The Experimental Biology at Postgenome Era
Having completed the sequencing of human genome and model animals and plants, molecular biology is shifting to a new era decoding the modulation mechanism of entire process of micro molecular activities led by gene expression and signal regulation. At present, the postgenome era molecular biology is theoretically and experimentally brewing a new breakthrough. Its core is to break away from the framework of original "gene centered" or "genetic determinism", and places the development of the postgenome on the basis of two new and important experimental understandings.
First, only the bionetworks form the micro modulation basis of all life activities at cell-level. The importance of bionetworks has been greatly enhanced, and the bionetworks become the new objects for theoretical and experimental research of molecular modulation mechanisms.
Second, the process that gene expressed to phenotype is regulated and influenced by both internal and external environmental factors. The concept "DNA sequence is the deterministic blueprint for growth" has been changed, and how to integrate internal and external signals to regulate gene expression becomes the new core issue.
At present, about the new theories and methods of postgenome research, there are two brewing developmental directions requiring attention.
One is the new research framework of "systems biology". It is hoped that through the systematic simulation and interference experiment, they can holistically and synthetically achieve the computing and modeling of huge quantity of data, to push the gene annotation up to the network and system level.
The other is the new theoretical innovation of "phenotypic plasticity". Namely, the discoveries that “the individuals of the same genotype in their lifetime can actively make multiform responses (in the broad sense of physiological phenotype) to the changeful environmental signals” provide a new perspective for understanding the postgenome.
These two directions are quite different in the origin, historical background, disciplinary character and experimental basis. And there still have many problems in their theoretical and methodological explorations.
Recently, a research monograph The Deep Structure of Being: the Development of Neo-adaptationist Biology and the New Synthesis (3 volumes in total) was formally published by BECG. And at the same time, a theoretical report titled "The Theoretical Advancement of the Neo-adaptationist Biology" was published on the "Lorenz Memorial Lecture", giving a concise introduction of their summarizing studies on phenotypic plasticity and other branches of the neo-adaptationism.
The report pointed out that the neo-adaptationist physiological theories are gradually converged towards two aspects, resistance theory and plasticity theory. The formation of phenotypic plasticity idea, in particular, has more important theoretical value.
In the traditional doctrine, genotype is the basic unit of biological adaptation, and the dispersing efficiency of the genotypes in relation to the niches is the interpretation standard of biological adaptation. However phenotypic plasticity studies have provided different empirical evidences, that a particular genotype in different environments can express different phenotypes. Phenotype uses its plasticity to respond to the changes in the environment. Evidences have shown that the genetic restriction to phenotype is not as simple and direct as originally imagined. Organisms maintain their optimality through the conversion of different phenotypes and different responses to the environmental conditions. In other words, in the traditional doctrine, one genotype can only form a set of phenotype system; while the new theory believes that a genotype can form multi-sets of phenotype system. This change of biological theory breaks away from the original "gene–phenotype" theory, going toward the "gene–strategy–phenotype" new theoretical direction.
At the same time, phenotypic plasticity studies also have important impact on the traditional genetic determinism for organism’s development. Phenotypic plasticity study found the process that gene expressed to phenotype is regulated and influenced by both internal and external environmental factors. This reveals the role play by concrete environmental changes in the complex physiological process of phenotypic regulation. Because of the plasticity research, developmental biology has moved beyond the traditional view that "DNA sequence is the deterministic blueprint for growth", and understood organism as a developmental system that continuously integrating both internal and external signals to regulate gene expression. At present, the study of developmental plasticity is leading the developmental biology towards the specific processes of the bionetwork-centered molecular transmission mechanism and the regulation system.
The report concluded that the phenotypic plasticity research is essentially the study of "phenotypic optimality". That is the micro-physiology based eco-optimality comparative analysis of intraspecific phenotypic physiology. At present this new research methods are trying hard to move away from the fitness framework of the Modern Synthesis. The study of adaptation hence would be perfectly associated both with phenotypic and physiological researches. In a short time nearly three decades, phenotypic plasticity study has pushed the both physiology and ecology of phenotypic adaptation to a new level. And it has acquired a great number of experimental discoveries.
BECG further suggested that "phenotypic optimality" research might provide physiology-level possibilities for explaining adaptation. This is manifested in two new understandings: 1) intraspecific ecological optimality of phenotypic physiology can be explained as: with the genotype’s phenotypic transforms, organism respectively forms the efficiency advantage corresponding to the niche variables. 2) The transformative activities of functional operation can be interpreted as: organism’s component behavior is subjected to different modulation restrictions in different phenotypic transforms. To sum up, the physiology of adaptation can be expressed as: organism uses the different holistically and self-modulatedly formed restrictions to component behavior, to create different phenotypic advantages that aiming at different niche conditions.
In this way, BECG formally proposed a new reductionist, physiology-ecology joint interpretation based understanding about adaptation. This new reductionist method is based on a new bio-structure view, a new constructional understanding of being. Namely, in specific physiology-ecology phenotypic variants, any component of organism has certain implication and joint resistance advantage corresponding to the environmental pressures. That is to say, a set of specific components constitute some physiological phenotypic variant with specific eco-efficiency advantages. These components are specifically limited and restricted during the process they take part in the formation of the variant. In this way, adaptation problem would be reduced to a joint relation of phenotypic variants unit among concrete components, and then the structural relations among different phenotypic variant units would be formed. Thus, through the intraspecific comparative study, bio-adaptation can be transferred into a new structural analysis. This "structure" is totally different from the functional “structure” in traditional biology, and BECG named it as "deep structure of being".
Based on this new principle and understanding, BECG further integrated phenotypic plasticity and other theories into the deep structure theory in its works. They suggested that experimental studies of phenotypic plasticity, by comparing the conversion of different phenotypes (especially at micro-physiological level) in response to specific environmental conditions, could discover the optimality of different strategies, and these methods could be furthered to deep structure experimental analysis. It can be used as an analytical tool for solving the bionetwork and molecular modulation mechanism. Among them, the strategy comparison of phenotypic changes being transferred to deep structure analysis can be of help in detecting the dividing-line of molecular bionetwork; while the comparative analysis between the ecology and the physiology being transferred to deep structure analysis can help to solve the problem how the external factors and internal genes micro-physiologically form the life modulation mechanism. Deep structure analysis finds a new path for the development of the postgenome experimental biology. The newly published Deep Structure of Being, in chapter 22, 23 and 24 of 3rd volume, has detailed the application of deep structure theories and experimental methods in the molecular bionetwork studies.
In the attachment it talks about the genotype determining a range of phenotypes that are dependent on external factors as well as internal ones. The phenotype, plastic or not is still dependent on the genotype. The point is that it is not always a simple case of genotype A determines phenotype A. It may lead to phenotypes A1, A2, A3, A4 or A5.
Again, they are saying it is not a simple one blueprint determines one phenotype. No where does it claim, as you did, that we need to rethink evolution.
This is a strategy that can work if delaying procreation will result in a better chance for success later. A large number of offspring may or may not result in better success depending on the circumstances. Your attached article says nothing about changing our ideas on reproductive success, and you have offered no viable alternative.
My understanding of this article is different from you.
In sum, there are two focus(points) in the discussion between us. Are genes the only factors that determine the phenotype, or not? Is the reproductive success the only criteria of adaptation, or not?
First of all, the deep-structure theory suggests that genes is not the only decisive factor on the phenotype,physiological factor, is another important one. Phenotypic changes are not only dominated by genes, but also by the physiological mechanism. In other words, phenotype sometimes directly are modulated by the physiological systems. For example, a large number of behavioral Phenotypes are directly controlled by the neurophysiological modulation. The phenotype of these acts have an important effect for life's adaptive survival, but they are not able to be direct inherited.they are only transmited through culture and social learning. How do you explain this problem?
Moreover, the deep-structure theory suggests that reproductive success is not the only
criterion to measure adaptability. For example, life expectancy , such a phenotype study shows that the length of life is itself a good indication of adaptation, which indicates the viability of life in the environment.It is thought-provoking that long-lived species, their reproductive rates are relatively lower. If you do the same reasoning, one species which has an infinitely long life, its reproduction rate should be zero. This assumption shows that in the "super-life" conditions, the reproduction does not make any sense..Do you also used it to do adaptive measure?
Recommend BECG's articles http://www.brainecology.net/ktjh/
Sure, learned behavior is important with some "higher" species such as ours. These behaviors are in a sense inherited culturally from parent to offspring. Yet, the capacity to learn is itself determined by genetics... is it not?
Those species with a long lifespan and slow reproductive rate are the most vulnerable to extinction. Ask yourself why there are no mammoths, rhinos or horses native to North America any longer? They all died out and horses had to be re-introduced from the Europeans. What are the most successful organisms on earth? Bacteria. They also have the shortest reproductive turn over. Are you going to claim they are poorly adapted? They were here before us and will be here after we are gone. You mentioned immortal species ... why aren't there any? Answer that question, and you will have the answer to your question as well.
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